Lakhansing Pardeshi
July 25, 2024
Pangenome statistics: Homology group counts for the genus pangenome and individual species pangenome
Homology group copy number variation across 454 genomes in the pangenome. This is a big file and hence refer to the raw file at location …
---
title: "Supplementary tables"
author: "Lakhansing Pardeshi"
date: "`r Sys.Date()`"
format:
html:
embed-resources: true
df-print: paged
knitr:
opts_chunk:
fig.height: 7
---
```{r}
#| label: setup
#| echo: false
#| warning: false
suppressPackageStartupMessages(library(tidyverse))
suppressPackageStartupMessages(library(org.Pectobacterium.spp.pan.eg.db))
suppressPackageStartupMessages(library(DT))
rm(list = ls())
source("https://raw.githubusercontent.com/lakhanp1/omics_utils/main/RScripts/utils.R")
source("scripts/utils/config_functions.R")
source("scripts/utils/homology_groups.R")
################################################################################
set.seed(124)
confs <- prefix_config_paths(
conf = suppressWarnings(configr::read.config(file = "project_config.yaml")),
dir = "."
)
pangenome <- confs$data$pangenomes$pectobacterium.v2$name
panConf <- confs$data$pangenomes[[pangenome]]
panOrgDb <- org.Pectobacterium.spp.pan.eg.db
```
::: {.panel-tabset}
## Table 1
```{r}
#| echo: false
#| column: screen-inset-right
s1 <- suppressMessages(readr::read_csv(panConf$files$metadata)) %>%
dplyr::select(-starts_with("nodepath."))
DT::datatable(
data = s1,
rownames = FALSE,
filter = "top",
class = 'compact hover',
extensions = c('KeyTable', 'Scroller', 'Select', 'SearchBuilder', 'FixedColumns'),
options = list(
autoWidth = FALSE,
dom = 'Qlfrtip',
scrollX = TRUE,
fixedColumns = list(leftColumns = 2),
keys = TRUE,
scroller = TRUE,
scrollY = 600
),
selection = 'none'
)
```
## Table 2
Pangenome statistics: Homology group counts for the genus pangenome and
individual species pangenome
```{r}
#| echo: false
#| column: screen-inset-right
s2 <- suppressMessages(
readr::read_tsv(confs$analysis$homology_groups$files$spp_group_stats)
)
DT::datatable(
data = s2,
rownames = FALSE,
filter = "top",
class = 'compact hover',
extensions = c('KeyTable', 'Scroller', 'Select', 'SearchBuilder', 'FixedColumns'),
options = list(
autoWidth = FALSE,
dom = 'Qlfrtip',
scrollX = TRUE,
fixedColumns = list(leftColumns = 2),
keys = TRUE,
scroller = TRUE,
scrollY = 600
),
selection = 'none'
)
```
## Table 3
Homology group copy number variation across 454 genomes in the pangenome. This
is a big file and hence refer to the raw file at location ...
```{r}
#| echo: false
#| eval: false
#| column: screen-inset-right
s3 <- homology_groups_mat(pandb = panOrgDb, type = "cnv")
s3 <- tibble::as_tibble(s3, rownames = "genomeId")
DT::datatable(
data = s3,
rownames = FALSE,
filter = "top",
class = 'compact hover',
extensions = c('KeyTable', 'Scroller', 'Select', 'SearchBuilder', 'FixedColumns'),
options = list(
autoWidth = FALSE,
dom = 'Qlfrtip',
scrollX = TRUE,
fixedColumns = list(leftColumns = 2),
keys = TRUE,
scroller = TRUE,
scrollY = 600
),
selection = 'none'
)
```
## Table 4
```{r}
#| echo: false
#| column: screen-inset-right
s4 <- suppressMessages(
readr::read_tsv(confs$analysis$homology_groups$files$spp_group_go)
) %>%
dplyr::filter(SpeciesName == "pangenome") %>%
dplyr::select(-SpeciesName)
DT::datatable(
data = s4,
rownames = FALSE,
filter = "top",
class = 'compact hover',
extensions = c('KeyTable', 'Scroller', 'Select', 'SearchBuilder', 'FixedColumns'),
options = list(
autoWidth = FALSE,
dom = 'Qlfrtip',
scrollX = TRUE,
fixedColumns = list(leftColumns = 2),
keys = TRUE,
scroller = TRUE,
scrollY = 600
),
selection = 'none'
)
```
## Table 5
```{r}
#| echo: false
#| column: screen-inset-right
s5 <- suppressMessages(
readr::read_tsv(confs$analysis$prophages$summary$files$prophage_stats_species)
)
DT::datatable(
data = s5,
rownames = FALSE,
filter = "top",
class = 'compact hover',
extensions = c('KeyTable', 'Scroller', 'Select', 'SearchBuilder', 'FixedColumns'),
options = list(
autoWidth = FALSE,
dom = 'Qlfrtip',
scrollX = TRUE,
fixedColumns = list(leftColumns = 2),
keys = TRUE,
scroller = TRUE,
scrollY = 600
),
selection = 'none'
)
```
## Table 6
```{r}
#| echo: false
#| column: screen-inset-right
s6 <- suppressMessages(readr::read_tsv(confs$data$prophages$files$data)) %>%
dplyr::select(-contig_id, genomeId, everything())
DT::datatable(
data = s6,
rownames = FALSE,
filter = "top",
class = 'compact hover',
extensions = c('KeyTable', 'Scroller', 'Select', 'SearchBuilder', 'FixedColumns'),
options = list(
autoWidth = FALSE,
dom = 'Qlfrtip',
scrollX = TRUE,
fixedColumns = list(leftColumns = 2),
keys = TRUE,
scroller = TRUE,
scrollY = 600
),
selection = 'none'
)
```
## Table 7
```{r}
#| echo: false
#| column: screen-inset-right
s7 <- suppressMessages(
readr::read_tsv(confs$analysis$prophages$files$clusters)
) %>%
dplyr::select(-starts_with("nodepath."))
DT::datatable(
data = s7,
rownames = FALSE,
filter = "top",
class = 'compact hover',
extensions = c('KeyTable', 'Scroller', 'Select', 'SearchBuilder', 'FixedColumns'),
options = list(
autoWidth = FALSE,
dom = 'Qlfrtip',
scrollX = TRUE,
fixedColumns = list(leftColumns = 2),
keys = TRUE,
scroller = TRUE,
scrollY = 600
),
selection = 'none'
)
```
:::